5MC6: 40S ribosomal protein S3
Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae. Determined by electron microscopy at 3.8 Å resolution. Released 18 Jan 2017.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 87
- Atoms
- 229,285
- Mol. weight
- 3599.38 kDa
- Released
- 18 Jan 2017
Explore 5MC6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5MC6 contains 610 α-helices and 668 β-strands across 80 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain a: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 11 |
| β-strand | 6-8 | 3 | 11 |
| α-helix | 13-14 | 2 | |
| β-strand | 15-16 | 2 | 12 |
| β-strand | 23-24 | 2 | 12 |
| β-strand | 32-37 | 6 | 13 |
| β-strand | 40 | 1 | 14 |
| β-strand | 43 | 1 | 14 |
| β-strand | 50-55 | 6 | 13 |
| α-helix | 57-62 | 6 | |
| α-helix | 65-76 | 12 | |
Chain A: 6 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| β-strand | 34-41 | 8 | 7 |
| β-strand | 46-52 | 7 | 7 |
| α-helix | 65-77 | 13 | |
| β-strand | 84-86 | 3 | 7 |
| β-strand | 89-90 | 2 | 7 |
| α-helix | 91 | 1 | |
| α-helix | 98-112 | 15 | |
| α-helix | 115-128 | 14 | |
| β-strand | 131-138 | 8 | 8 |
| β-strand | 150-154 | 5 | 8 |
| α-helix | 161-166 | 6 | |
| β-strand | 169-176 | 8 | 8 |
| β-strand | 181-190 | 10 | 8 |
| β-strand | 208 | 1 | 9 |
| β-strand | 223 | 1 | 10 |
Chain AA: 12 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 51 | 1 | 125 |
| α-helix | 54-68 | 15 | |
| β-strand | 70 | 1 | 126 |
| α-helix | 84-95 | 12 | |
| α-helix | 102-117 | 16 | |
| α-helix | 132 | 1 | |
| β-strand | 133-134 | 2 | 127 |
| α-helix | 136-144 | 9 | |
| β-strand | 150-153 | 4 | 127 |
| α-helix | 166-172 | 7 | |
| β-strand | 177-179 | 3 | 127 |
| α-helix | 183-190 | 8 | |
| β-strand | 197-200 | 4 | 127 |
| α-helix | 209-221 | 13 | |
| α-helix | 223-225 | 3 | |
| α-helix | 226-231 | 6 | |
| β-strand | 235 | 1 | 126 |
| α-helix | 240-246 | 7 | |
| α-helix | 247-251 | 5 | |
Chain AB: 2 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-18 | 2 | 136 |
| β-strand | 21-25 | 5 | 137 |
| β-strand | 27 | 1 | 138 |
| β-strand | 31-39 | 9 | 137 |
| β-strand | 51-52 | 2 | 136 |
| β-strand | 57-65 | 9 | 137 |
| β-strand | 74-81 | 8 | 137 |
| β-strand | 85-87 | 3 | 139 |
| β-strand | 91-95 | 5 | 139 |
| β-strand | 98-102 | 5 | 137 |
| β-strand | 103 | 1 | 140 |
| β-strand | 109 | 1 | 140 |
| β-strand | 114 | 1 | 138 |
| β-strand | 118 | 1 | 141 |
| α-helix | 120-123 | 4 | |
| α-helix | 127-132 | 6 | |
| β-strand | 136 | 1 | 141 |
Chain AC: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-25 | 4 | |
| α-helix | 36-48 | 13 | |
| α-helix | 52-64 | 13 | |
| α-helix | 66-76 | 11 | |
| α-helix | 80-92 | 13 | |
| α-helix | 93-97 | 5 | |
Chain AD: 3 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 151 |
| β-strand | 6-11 | 6 | 152 |
| β-strand | 17-21 | 5 | 153 |
| β-strand | 24-28 | 5 | 153 |
| β-strand | 33-37 | 5 | 153 |
| β-strand | 44-49 | 6 | 152 |
| β-strand | 52-57 | 6 | 152 |
| β-strand | 60 | 1 | 151 |
| α-helix | 62-83 | 22 | |
| β-strand | 86-93 | 8 | 154 |
| β-strand | 100-104 | 5 | 155 |
| β-strand | 111-115 | 5 | 155 |
| β-strand | 124-127 | 4 | 155 |
| α-helix | 128-129 | 2 | |
| β-strand | 132-135 | 4 | 154 |
| β-strand | 143-148 | 6 | 154 |
| α-helix | 151-164 | 14 | |
| β-strand | 178-186 | 9 | 154 |
Chain AE: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 169 |
| β-strand | 12 | 1 | 169 |
| β-strand | 19-22 | 4 | 139 |
| β-strand | 29 | 1 | 139 |
| α-helix | 34-42 | 9 | |
| α-helix | 46-48 | 3 | |
| α-helix | 53-59 | 7 | |
| α-helix | 88-91 | 4 | |
Chain AF: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-8 | 4 | |
| β-strand | 16-17 | 2 | 181 |
| β-strand | 27-28 | 2 | 181 |
| β-strand | 33-34 | 2 | 181 |
| α-helix | 51-54 | 4 | |
| α-helix | 67-75 | 9 | |
72 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 18S ribosomal RNA | 2 | RNA | 1800 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
| 40S ribosomal protein S3 | A | protein | 240 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P05750 (AlphaFold model) |
| 40S ribosomal protein S5 | B | protein | 225 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26783 (AlphaFold model) |
| 40S ribosomal protein S10-A | C | protein | 105 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q08745 (AlphaFold model) |
| 40S ribosomal protein S12 | D | protein | 143 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P48589 (AlphaFold model) |
| 40S ribosomal protein S15 | E | protein | 142 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q01855 |
| 40S ribosomal protein S16-A | F | protein | 143 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX51 |
| 40S ribosomal protein S17-B | G | protein | 136 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P14127 |
| 40S ribosomal protein S18-A | H | protein | 146 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX55 |
| 40S ribosomal protein S19-A | I | protein | 144 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P07280 |
| 40S ribosomal protein S20 | J | protein | 121 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38701 |
| 40S ribosomal protein S25-A | K | protein | 108 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q3E792 |
74 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>5MC6_1 18S ribosomal RNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCG
AUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUG
UGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUA
UUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCU
UAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCC
CUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGC
CGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAU
UGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCC
UGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGG
AUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCA
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 2 (A), FASTA
>5MC6_2 40S ribosomal protein S3 (chains A)
MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG
ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQG
VLGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA
Sequence of entity 3 (B), FASTA
>5MC6_3 40S ribosomal protein S5 (chains B)
MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD
YVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDI
INVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAR
EAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 4 (C), FASTA
>5MC6_4 40S ribosomal protein S10-A (chains C)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERNPTQRPQRRY
Sequence of entity 5 (D), FASTA
>5MC6_5 40S ribosomal protein S12 (chains D)
MSDVEEVVEVQEETVVEQTAEVTIEDALKVVLRTALVHDGLARGLRESTKALTRGEALLV
VLVSSVTEANIIKLVEGLANDPENKVPLIKVADAKQLGEWAGLGKIDREGNARKVVGASV
VVVKNWGAETDELSMIMEHFSQQ
Sequence of entity 6 (E), FASTA
>5MC6_6 40S ribosomal protein S15 (chains E)
MSQAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKL
RAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFS
ITYTPVRHGRAGATTSRFIPLK
Sequence of entity 7 (F), FASTA
>5MC6_7 40S ribosomal protein S16-A (chains F)
MSAVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKF
SNIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIAD
SRRPEPKKFGGKGARSRFQKSYR
Sequence of entity 8 (G), FASTA
>5MC6_8 40S ribosomal protein S17-B (chains G)
MGRVRTKTVKRASKALIERYYPKLTLDFQTNKRLCDEIATIQSKRLRNKIAGYTTHLMKR
IQKGPVRGISFKLQEEERERKDQYVPEVSALDLSRSNGVLNVDNQTSDLVKSLGLKLPLS
VINVSAQRDRRYRKRN
Sequence of entity 9 (H), FASTA
>5MC6_9 40S ribosomal protein S18-A (chains H)
MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGE
LTQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIR
AHRGIRHFWGLRVRGQHTKTTGRRRA
Sequence of entity 10 (I), FASTA
>5MC6_10 40S ribosomal protein S19-A (chains I)
MPGVSVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAAS
VARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKG
GRRISENGQRDLDRIAAQTLEEDE
Sequence of entity 11 (J), FASTA
>5MC6_11 40S ribosomal protein S20 (chains J)
MSDFQKEKVEEQEQQQQQIIKIRITLTSTKVKQLENVSSNIVKNAEQHNLVKKGPVRLPT
KVLKISTRKTPNGEGSKTWETYEMRIHKRYIDLEAPVQIVKRITQITIEPGVDVEVVVAS
N
Sequence of entity 12 (K), FASTA
>5MC6_12 40S ribosomal protein S25-A (chains K)
MPPKQQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYV
SVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE
Primary citation
The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Schmidt, C., Kowalinski, E., Shanmuganathan, V. et al. Science (2016) 354:1431-1433. DOI 10.1126/science.aaf7520 · PubMed
Other PDB entries of the same protein (UniProt P05750 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
- 8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
- 8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
- 8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
- 8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
- 9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 7ZW0 2.4 Å, FAP-80S Complex - Rotated state
- 8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing
- 8T2Z 2.4 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
- 8T2X 2.46 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger…
- 9DOV 2.49 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 7ZUX 2.5 Å, Collided ribosome in a disome unit from S. cerevisiae
Browse structure collections
About this viewer
MolViewer shows 5MC6 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.